The feline major histocompatibility complex (MHC) has been studied using molecular techniques as an approach to comparative genome organization of this important gene cluster. The MHC in most mammals consists of two classes of genes, classes I and II, which play special roles in presenting antigens to T-cell receptors. Southern blotting analysis of class I genes of many species including human, mouse, and cat families (domestic cat, African cheetah, and lion) shows the correlation of the extent of restriction fragment length polymorphisms (RFLP), the functional diversity of the MHC molecules, and the allozyme variation in each species. Sequence analysis of eight different feline MHC (FLA) class I cDNA clones revealed strong conservation of invariant and variant amino acid residues in antigen-binding and T-cell recognition sites among human, mouse, and domestic cat. This evidence indicates that the domestic cat has a similar structure to the human HLA-A2 class I molecule, and its MHC class I molecules have highly polymorphic features like human and mouse. Further analysis revealed the participation of four major factors in the evolution of feline MHC class I genes. These include (1) a gradual accumulation of spontaneous mutational substitution, (2) negative selection for functional constraints of class I genes, (3) positive selection in favor of persistence of polymorphism, and (4) periodic intragenic and intergenic DNA recombination.